A prototype tool set to support machine-assisted annotation

BioNLP@HLT-NAACL 2012 - Workshop on Biomedical Natural Language Processing, Proceedings

Volumn , Issue , 2012, Pages 130-139

  South, Brett R ^a   Shen, Shuying ^a   Leng, Jianwei ^a   Forbush, Tyler B ^b   DuVall, Scott L ^a,b   Chapman, Wendy W ^c  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b IDEAS Center SLCVA Healthcare System   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LEARNING ALGORITHMS;

ANNOTATION TOOL; LABOUR-INTENSIVE; LARGE-SCALES; MACHINE-LEARNING; OPEN-SOURCE; PROCESSING MACHINES; PROTOTYPE TOOLS; REFERENCE STANDARD; SYSTEM LEARNING; TOOLSETS;

NATURAL LANGUAGE PROCESSING SYSTEMS;

EID: 85012913456     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (23)

1. Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjov, Ewan Klein, Michael Matthews, Stuart Roebuck, Richard Tobin, and Xinglong Wang. 2008. Assisted curation: does text mining really help? In: Proceedings of the Pacific Symposium on Biocomputing.
2. Wendy W. Chapman, David Chu, John N. Dowling. 2007. ConText: An Algorithm for Identifying Contextual Features from Clinical Text. In: ACL- 07 2007.
3. Carol Friedman, Hongfang Liu, Lyudmila Shagina, Stephen Johnson, George Hripcsak. 2001. Evaluating the UMLS as a source of lexical knowledge for medical language processing. In: Proc AMIA Symp, 2001: 189-93.
4. Karen Fort and Saggot B. 2010. Influence of Pre- Annotation on POS-tagged Corpus Development. In: Proceedings of the Fourth Linguistic Annotation Workshop. ACL 2010: 56-63.
5. Pei-Yun Hsueh, Prem Melville, Vikas Sindhwani. 2009. Data Quality from Crowdsourcing: A study of Annotation Selection Criteria. In: Proceedings of the NAACL HLT Workshop on Active Learning for Natural Language Processing. June 2009: 27- 35.
6. Danielle Mowery, Henk Harkema, Wendy W. Chapman. 2008. Temporal Annotation of Clinical Text. In: ACL-08 2008.
7. Mark A. Musen, John Gennari, Henrik Eriksson, Samson W. Tu, and Angel R. Puerta. 1995. PROTEGE-II: computer support for development of intelligent systems from libraries of components. In: Medinfo 1995.
8. Aurélie Névéol, Rezarta Islamaj-DoǦan, Zhiyong Lu. 2011. Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. In: J Biomed Inform. 2011 Apr; 44(2):310-8.
9. Stefanie Nowak and Stefan Ruger. 2010. How Reliable are Annotations via Crowdsourcing? A Study about Inter-Annotator Agreement for Multi-label Image Annotation. In: MIR 10 2010.
10. Philip V. Ogren. 2006. Knowtator a protege plug-in for annotated corpus construction. In: Proceedings of the 2006 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology, 2006: 273-5.
11. Philip V. Ogren, Guergana K. Savova, Christopher G. Chute. 2008. Constructing Evaluation Corpora for Automated Clinical Named Entity Recognition. In: Proceedings of the sixth international conference on Language Resources and Evaluation LREC 2008: 3143-3150.
12. Angus Roberts, Robert Gaizauskas, Mark Hepple, Neil Davis, George Demetriou, Yikun Guo, Jay Kola, Ian Roberts, Andrea Setzer, Archana Tapuria, Bill Wheeldin. 2007. The CLEF corpus: semantic annotation of clinical text. In: AMIA Annu Symp Proc, 625-9.
13. Angus Roberts, Robert Gaizauskas, Mark Hepple, George Demetriou, Yikun Guo, Ian Roberts, Andrea Setzer. 2009. Building a semantically annotated corpus of clinical texts. In: J Biomed Inform, 42(5): 950-66.
14. Ellen Riloff. 1993. Automatically constructing a dictionary for information extraction tasks. In: Proceedings of the Eleventh National Conference on Artificial Intelligence, 811-816.
15. Burr Settles, Mark Craven, and Lewis Friedland. 2008. Active Learning with Real Annotation Costs. In: Proceedings of the NIPS Workshop on Cost-Sensitive Learning. 2008.
16. Burr Settles. 2009. Active Learning Literature Survey. In: Computer Sciences Technical Report 1648. University of Wisconsin-Madison. 2009.
17. Brett R. South, Shuying Shen, F. Jeff Friedlin, Matthew H. Samore, and Stephane M. Meystre. 2010. Enhancing Annotation of Clinical Text using Pre- Annotation of Common PHI. In: AMIA Annu Symp Proc. 2010.
18. Brett R. South, Shuying Shen, Robyn Barrus, Scott L. DuVall, Ozlem Uzuner, and Charlene Weir. 2011. Qualitative analysis of workflow modifications used to generate the reference standard for the 2010 i2b2/VA challenge. In: AMIA Annu Symp Proc. 2011.
19. Özlem Uzuner, Imre Solti, Fei Xia, and Eithon Cadag. 2010. Community annotation experiment for ground truth generation for the i2b2 medication challenge. In: J Am Med Inform Assoc, 2010. 17(5):519-23.
20. Özlem Uzuner, Brett R. South, Shuying Shen, and Scott L. DuVall. 2011. 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text. In: JAMIA 18(5): 552-556.
21. Özlem Uzuner, Andreea Bodnari, Shuying Shen, Tyler B. Forbush, John Pestian, and Brett R. South. 2012. Evaluating the state of the art in coreference resolution for electronic medical records. In: JAMIA doi: 10.1136/amiajnl-2011-000784.
22. Aobo Wang, Cong Duy Vu Hoang, and Min-Yen Kan. 2010. Perspectives on Crowdsourcing Annotations for Natural Language Processing. In: CSIDM Project No. CSIDM-200805.
23. Alexander S. Yeh, Lynette Hirschman, and Alexander A. Morgan. 2003. Evaluation of text data mining for database curation: Lessons learned from the KDD challenge cup. In: Bioinformatics, 19(Suppl 1): i331-339, 2003.